The promise of targeted protein degradation approaches
Authors: Danette L. Daniels, Gopal P. Sapkota, Lyn H. Jones
Journal: Trends in Pharmacological Sciences (2023)

It is an exciting time to be in the targeted protein degradation (TPD) research field. TPD is a promising strategy in therapy development. Newer TPD technologies are being developed for the treatment of cancer and various diseases. Jerry Madukwe, the editor-in-chief of Trends in Pharmacological Sciences (TIPS), asked experts in the field from academia and industry to reflect on the global challenges in the field and what they see as its future. Danette Daniels Danette Daniels (DD): I was drawn to the field of TPD 8 years ago while working in the area of small-molecule inhibitors of chromatin regulatory targets. At the time, there was a collection of fantastic and specific chemical probes, yet, for many of these targets, inhibition alone was not sufficient to show the desired cellular outcomes and efficacy. Target degradation was the next logical step to try, but, in those early days, it was not even clear how broadly the TPD concept and modality could be applied. After testing numerous degraders against numerous targets along with the field, I then focused on understanding the different cellular modes of action of degraders. In my current role at Foghorn, the team and I apply these approaches and learnings for the development and characterization of highly efficacious degraders across numerous therapeutic programs. Gopal Sapkota Gopal Sapkota (GS): My research over the past decade has focused on dissecting molecular mechanisms of reversible protein phosphorylation and ubiquitylation in cell signaling. I was drawn to TPD as an excellent tool to decipher the functions of proteins that I was working on at the time. TPD is now an indispensable tool to study the function of potentially any intracellular protein, and for drug discovery. Lyn Jones Lyn Jones (LJ): Thirty years ago, I spent a year at Sandoz Pharma in Switzerland during my Bachelor’s degree developing rapamycin-derived molecular glues. The experience opened my eyes to the magic of small-molecule drugs, and to the emerging field of induced-proximity pharmacology. Through my career, I have focused on developing new therapeutic modalities to address the main reason for clinical failure: a lack of efficacy. TPD will no doubt help us expand the druggable proteome with the goal of advancing drug candidates with greater efficacy. LJ: Many molecular glue degraders (MGDs) were discovered serendipitously, whereas the mechanisms behind their phenotypic efficacy were revealed following many years of research. An opportunity in this area is to learn from, and exploit, their molecular modes of action so that more rational drug discovery approaches can be deployed in the future. By contrast, heterobifunctional chimeric degraders are created in a very modular fashion, but their physicochemistry is different to traditional drugs, which complicates property-based optimization. We need to develop our understanding of the pharmacokinetic/pharmacodynamic (PK/PD) relationships of these molecules, which will lead to more rational drug development. A key advantage of the modality is that protein degradation is a relatively simple pharmacological biomarker to measure in the clinic, which will expedite proof-of-mechanism studies and accelerate translation. GS: TPD as a concept has been applied successfully in the clinic. MGDs, such as the thalidomide analogs, are among the biggest selling anticancer drugs. The challenge with MGDs is they are hard to develop rationally, but much progress has been made recently around rational glue design. By contrast, proteolysis targeting chimeras (PROTACs) have revolutionized rational TPD and have entered clinical trials, but their bioavailability remains the main challenge because of their relatively larger molecular size. DD: The enormous opportunity in the TPD field is both the expansion of the target space and disease areas that we can now approach for therapeutic development. Our first clinical program at Foghorn was against a protein target, BRD9, which was not an enzymatic protein. Additionally, compounds targeting it were not previously approved, and preclinical studies showed that degradation was required for efficacy. Given that degraders, particularly heterobifunctional ones, are still in the early clinical stages, we don’t yet have many data available on their safety and efficacy. However, we will learn more in the coming years, as degraders are applied to indications beyond oncology. I also believe that studying and targeting the chromatin regulatory system at scale, in context, and in an integrated way brings tremendous potential to the field. GS: TPD is considered an exciting new modality in drug discovery because it allows the destruction of potentially any intracellular protein by hijacking the proteolytic machinery of the cell. The notion of TPD, that a bivalent molecule can recruit an E3 ubiquitin ligase to a neosubstrate for its ubiquitylation and degradation, can be applied, in principle, to recruiting any protein-modifying enzyme to a neosubstrate for functional modulation of the substrate. Small bifunctional molecules that can be applied for targeted protein post-translational modifications, such as dephosphorylation, open exciting avenues for novel medicines. DD: Degradation of key disease drivers will be essential, and perhaps the only option, for attacking particular indications or previously intractable targets. The question in the field now turns to what the best degrader approach is. Should it be a molecular glue or a heterobifunctional, or perhaps even an antibody–drug conjugate (ADC)-PROTAC, to limit toxicity? Are cereblon (CRBN) or Von Hippel-Lindau (VHL) the best E3 ligase recruiters to utilize, or should we be exploring others? Each of these questions brings a different strategy and set of risks to the clinic. However, the exciting part is that research on these different approaches is exploding; thus, for any given program, there are multiple paths one could take. LJ: Most importantly, degradation needs to bring some advantage over more traditional methods of target perturbation. For example, CRBN-based molecular glues degrade zinc finger transcription factors, which have been very difficult to drug because they lack small molecule-binding pockets. Certain degrader modalities are catalytic in nature, but this key feature has been relatively understudied and underexploited. Functional efficacy that derives only from fractional engagement of the target may enhance PK/PD profiles and lead to the development of anticancer and anti-infective agents with improved mutational resilience. Finally, I am intrigued by the potential of covalent E3 modulators to synthetically re-engineer protein surfaces and so mediate protein interactions in new ways. LJ: Most of the degraders in clinical trials are CRBN modulators. Moreover, there is also a relatively limited diversity of targets being degraded. Arguably, the field has yet to realize the full potential of drugging the ‘undruggable’. There are considerable activities in both industry and academia to expand the approach to establish greater diversity in the E3 ligase and therapeutic target. For example, resistance emerges in cancer through downregulation of CRBN and, thus, the community is trying to advance degraders that hijack essential E3s. It will also be exciting to see protein-based platforms develop in the coming years too as these have the potential to effectively address membrane proteins. DD: With the emergence of so many induced proximity agents and modalities, there is a significant knowledge gap in what will be broadly applicable and translatable to the clinic. The next several years will be important for our understanding of degrader performance across a significant number of targets and indications. Increasing our understanding of the best dosing regimens and routes of administration will be helpful for future development of medicines. For those indications for which there are approved inhibitors, we need a better understanding of how degraders are overcoming the challenges presented by the inhibitors, including resistance and efficacy. GS: There are many facets of TPD that we still do not understand. Some of these include understanding of and improving optimal chemical properties of degraders, determinants of intracellular PK for optimal TPD, defining the best E3 ligases for TPD, understanding how target protein context (such as its subcellular localization and nature of the macromolecular complex it is part of) affects degradation, understanding degrader mode of action, ensuring efficacy and specificity of TPD, and improving oral bioavailability of degraders. There is an over-reliance on VHL and CRBN as the main E3 ligases hijacked for TPD as ligands against other E3 ligases are limited. Future work should aim to address the issues highlighted earlier and seek to expand the arsenal of E3 ubiquitin ligases that can be harnessed for TPD. GS: Integrating technological advances made in other fields, such as proteomics, genome editing, and sequencing, and artificial intelligence and machine learning, in TPD workflows, from development of degraders all the way to their application, will advance the field of TPD. DD: In the early days, those of us working in TPD were making degraders to everything for which we had target binders just to see whether we could have success degrading targets. Now, we need to focus on the biology and why we must have the degrader. We need to take the risk of drugging targets that do not have known binding ligands or perhaps even domains that have never been drugged. Foghorn has one such program with our ARID1B degrader efforts. This is an excellent example of a protein that is neither an enzyme nor has defined druggable domains, yet, if a degrader to it could be developed, it could have significant therapeutic benefit across multiple oncology indications. We have recently disclosed binders to ARID1B for which we can begin to build degraders. More examples like this will push the field forward and deliver on the big promise of TPD for addressing previously undruggable targets. LJ: Public–private partnerships may help move the field forward by providing a forum to share precompetitive data and knowledge. For example, I co-chair the Targeted Protein Degradation Safety Committee run by the non-profit Health and Environmental Sciences Institute (HESI). Our mission is to advance effective translational safety assessments of degraders through an international network across industry, academia, and health agencies, and I think that we have made great progress. Additionally, I would like to see more profiling data, using functional genomics and proteomics, in the public domain to help us understand the breadth of protein degradability, which can impact therapeutic target selection and off-target identification. DD: Common goals and purpose are key! Understanding of target biology and connection to disease are so critical for all of our programs and where I see partnerships between academia and industry providing the greatest benefit. By combining resources and different areas of expertise, as well as sharing tool compounds, the science can be advanced more rapidly than either group working alone. GS: I think there are many examples of great collaborations between industry and academia already taking place within the TPD arena. I have been to many TPD conferences where there has been outstanding participation from both industry and academia. From experience, I can say that implementing and undertaking robust research practices and sharing quality tools, reagents, and reliable and reproducible data openly with colleagues from industry and academia promote productive collaborations. I have been fortunate to have been part of many exciting and fruitful collaborations with several pharmaceutical partners. LJ: Always start with the end in mind. It is important to ensure that everyone is on the same page regarding the objectives, accountabilities are clearly communicated, and a structure is created that ensures risks and rewards are shared. The industrial group must bring something other than funding to the partnership, and a relationship should be developed that fosters opportunities for the expertise of both parties to synergize. Specifically in targeted protein degradation, there are clearly emerging ways to treat certain diseases that may not appear to directly satisfy the commercial interests of industry in the short term. Collaborations in such areas though would progress the fundamental science and lead to therapeutic benefit in the future.